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Sample GSM3934951

Query DataSets for GSM3934951

Status

Public on Sep 04, 2020

Title

YueLab-H3K4me3-embryonic-Brain-rep2

Sample type

SRA

Source name

Tissue

Organism

Danio rerio

Characteristics

strain: Tuebingen
tissue: embryonic-Brain
chip-seq antibody: H3K4me3 antibody (EMD Millipore, 07-496)

Growth protocol

Embryonic Tuebingen zebrafish were raised under standard laboratory conditions

Extracted molecule

genomic DNA

Extraction protocol

Zebrafish embryonic tissue ChIP-seq was performed similarly to the adult tissue with a few modifications. For embryonic trunk, 50 trunks of 1 dpf embryos were dissected and digested in 500 µL of 0.25% trypsin at room temperature for 20 min. The reaction was then neutralized with FBS. Trunk cells were washed once with cold 1X PBS and cross-linked with 1% formaldehyde at room temperature for 12 min. For embryonic neuronal cells, Tg(Huc:Kaede) transgenic fish were crossed with wildtype Tuebingen fish. At 1 dpf, embryos were checked under the fluorescence microscope and green positive embryos were selected, dechorionated and pipetted in calcium free Ringer's solution to remove yolk. Supernatant was removed and 500 µL of 0.25% trypsin was added to digeste embryos at room temperature for 20 min. Neutralized with 500 µL of FBS and washed once with cold 1X PBS, digested cells were then cross-linked with 1% formaldehyde at room temperature for 12 min. Cells were then sorted and only green fluoresced cells, which corresponded to embryonic neuronal cells, were collected .
To prepare the library, eluted chromatin was reverse crosslinked and purified by phenol-chloroform extraction. Then DNA was end-repaired by END-IT DNA end-repair kit (Epicentre, ER81050) according to kit’s protocol, added A using Klenow fragment (3’->5’ exo-) (NEB, M0212S), ligated with Illumina TruSeq adaptor (Illumina, FC-121-3001) and subsequently amplified by PCR (Roche, kk2601). The quality and quantity of all the libraries were checked using BioAnalyzer High Sensitivity DNA Kit (Agilent). The libraries were sequenced on Illumina HiSeq 2500 with reads length of 2X 50 bp or 2X 100 bp.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina Genome Analyzer

Description

YueLab-ChIP-seq-embryonic-Brain_H3K4me3_merged.narrowPeak

Data processing

RNA-seq reads were aligned to zv10 genome assembly using STAR;
ChIP-seq and ATAC-seq reads were aligned to zv10 genome assembly using BWA
HiC reads were aligned to zv10 genome assembly using Bowtie2
The TPM value of gene expression was caculated using RSEM
ChIP-seq and ATAC-seq peaks were called using MACS2 with the following setting: ChIP-seq q-value <10e-2, p-value<10e-5, Change>1,FC>2. ATAC-seq: q-value<10e-2 and p-value<10e-5
HiC matrix was generated using HiC-Pro
Genome_build: zv10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi-C for each Sample.**All replicates were merged

Submission date

Jul 09, 2019

Last update date

Sep 04, 2020

Contact name

Yu Luan

E-mail(s)

yu.luan@northwestern.edu

Organization name

Northwestern University Feinberg School of Medicine

Department

Department of Biochemistry and Molecular Genetics